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fixed the header file for mpi3

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This commit is contained in:
azusayamaguchi 2017-07-11 14:15:08 +01:00
parent 8a4714a4a6
commit dc6f078246
2 changed files with 18 additions and 8 deletions
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8
configure.ac
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@ -51,6 +51,7 @@ AC_CHECK_HEADERS(malloc/malloc.h)
AC_CHECK_HEADERS(malloc.h) AC_CHECK_HEADERS(malloc.h)
AC_CHECK_HEADERS(endian.h) AC_CHECK_HEADERS(endian.h)
AC_CHECK_HEADERS(execinfo.h) AC_CHECK_HEADERS(execinfo.h)
AC_CHECK_HEADERS(numaif.h)
AC_CHECK_DECLS([ntohll],[], [], [[#include <arpa/inet.h>]]) AC_CHECK_DECLS([ntohll],[], [], [[#include <arpa/inet.h>]])
AC_CHECK_DECLS([be64toh],[], [], [[#include <arpa/inet.h>]]) AC_CHECK_DECLS([be64toh],[], [], [[#include <arpa/inet.h>]])
@ -186,9 +187,14 @@ Info at: http://usqcd.jlab.org/usqcd-docs/c-lime/)])
AC_SEARCH_LIBS([crc32], [z], AC_SEARCH_LIBS([crc32], [z],
[AC_DEFINE([HAVE_ZLIB], [1], [Define to 1 if you have the `LIBZ' library])] [AC_DEFINE([HAVE_ZLIB], [1], [Define to 1 if you have the `LIBZ' library])]
[have_zlib=true], [have_zlib=true] [LIBS="${LIBS} -lz"],
[AC_MSG_ERROR(zlib library was not found in your system.)]) [AC_MSG_ERROR(zlib library was not found in your system.)])
AC_SEARCH_LIBS([move_pages], [numa],
[AC_DEFINE([HAVE_LIBNUMA], [1], [Define to 1 if you have the `LIBNUMA' library])]
[have_libnuma=true] [LIBS="${LIBS} -lnuma"],
[AC_MSG_WARN(libnuma library was not found in your system. Some optimisations will not apply)])
AC_SEARCH_LIBS([H5Fopen], [hdf5_cpp], AC_SEARCH_LIBS([H5Fopen], [hdf5_cpp],
[AC_DEFINE([HAVE_HDF5], [1], [Define to 1 if you have the `HDF5' library])] [AC_DEFINE([HAVE_HDF5], [1], [Define to 1 if you have the `HDF5' library])]
[have_hdf5=true] [have_hdf5=true]

18
lib/communicator/Communicator_mpi3.cc
View File

@ -38,7 +38,9 @@ Author: Peter Boyle <paboyle@ph.ed.ac.uk>
#include <sys/shm.h> #include <sys/shm.h>
#include <sys/mman.h> #include <sys/mman.h>
#include <zlib.h> #include <zlib.h>
#ifdef HAVE_NUMAIF_H
#include <numaif.h> #include <numaif.h>
#endif
#ifndef SHM_HUGETLB #ifndef SHM_HUGETLB
#define SHM_HUGETLB 04000 #define SHM_HUGETLB 04000
#endif #endif
@ -216,6 +218,8 @@ void CartesianCommunicator::Init(int *argc, char ***argv) {
if ( ptr == MAP_FAILED ) { perror("failed mmap"); assert(0); } if ( ptr == MAP_FAILED ) { perror("failed mmap"); assert(0); }
assert(((uint64_t)ptr&0x3F)==0); assert(((uint64_t)ptr&0x3F)==0);
// Try to force numa domain on the shm segment if we have numaif.h
#ifdef HAVE_NUMAIF_H
int status; int status;
int flags=MPOL_MF_MOVE; int flags=MPOL_MF_MOVE;
#ifdef KNL #ifdef KNL
@ -225,13 +229,13 @@ void CartesianCommunicator::Init(int *argc, char ***argv) {
int nodes=r; // numa domain == MPI ID int nodes=r; // numa domain == MPI ID
#endif #endif
unsigned long count=1; unsigned long count=1;
for(uint64_t page=0;page<size;page+=4096){ for(uint64_t page=0;page<size;page+=4096){
void *pages = (void *) ( page + (uint64_t)ptr ); void *pages = (void *) ( page + (uint64_t)ptr );
uint64_t *cow_it = (uint64_t *)pages; *cow_it = 1; uint64_t *cow_it = (uint64_t *)pages; *cow_it = 1;
ierr= move_pages(0,count, &pages,&nodes,&status,flags); ierr= move_pages(0,count, &pages,&nodes,&status,flags);
if (ierr && (page==0)) perror("numa relocate command failed"); if (ierr && (page==0)) perror("numa relocate command failed");
} }
#endif
ShmCommBufs[r] =ptr; ShmCommBufs[r] =ptr;
} }